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annotate map_ensembl_transcripts.xml @ 21:d6b961721037

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Miller Lab Devshed version 4c04e35b18f6
author Richard Burhans <burhans@bx.psu.edu>
date Mon, 05 Nov 2012 12:44:17 -0500
parents 8ae67e9fb6ff
children
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1 <tool id="gd_new_oscar" name="Get Pathways" version="1.0.0">
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2 <description>: Look up KEGG pathways for given Ensembl transcripts</description>
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3
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4 <command interpreter="python">
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5 rtrnKEGGpthwfENSEMBLTc.py
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6 "--loc_file=${GALAXY_DATA_INDEX_DIR}/gd.oscar.loc"
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7 "--species=${input.metadata.dbkey}"
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8 "--input=${input}"
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9 "--posENSEMBLclmn=${ensembl_col}"
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10 "--output=${output}"
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11 </command>
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12
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13 <inputs>
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14 <param name="input" type="data" format="tabular" label="Dataset" >
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15 <validator type="unspecified_build" message="This dataset does not have a database/build and cannot be used with this tool" />
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16 </param>
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17 <param name="ensembl_col" type="data_column" data_ref="input" label="Column with ENSEMBL transcript ID" />
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18 </inputs>
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19
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20 <outputs>
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21 <data name="output" format="tabular" />
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22 </outputs>
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23
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24 <!--
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25 <tests>
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26 <test>
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27 <param name="input" value="test_in/ensembl.tabular" ftype="tabular">
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28 <metadata name="dbkey" value="canFam2" />
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29 </param>
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30 <param name="ensembl_col" value="1" />
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31
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32 <output name="output" file="test_out/map_ensembl_transcripts/map_ensembl_transcripts.tabular" />
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33 </test>
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34 </tests>
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35 -->
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36
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37 <help>
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38
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39 **Dataset formats**
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40
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41 The input and output datasets are in tabular_ format.
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42 The input dataset must have a column with an ENSEMBL transcript ID and have
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43 the database/build set. Even though positions are not needed the correct
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44 database/build must be given to look up the pathways.
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45 The output dataset will have added columns for the pathway.
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46 (`Dataset missing?`_)
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47
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48 .. _tabular: ./static/formatHelp.html#tab
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49 .. _Dataset missing?: ./static/formatHelp.html
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50
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51 -----
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52
14
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53 **What it does**
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54
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55 Adds the fields "KEGG gene ID" and "KEGG pathways" to an input table of ENSEMBL
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56 transcript IDs. A "U" in the KEGG gene ID field indicates that the
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57 tool cannot link the ENSEMBL transcript ID to a KEGG gene ID.
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58 An "N" in the pathway field means the KEGG pathway is unknown.
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59
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60 -----
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61
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62 **Example**
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63
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64 - input::
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65
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66 ENSCAFT00000000001
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67 ENSCAFT00000000144
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68 ENSCAFT00000000160
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69 ENSCAFT00000000215
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70 etc.
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71
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72 - output::
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73
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74 ENSCAFT00000000001 476153 cfa00230=Purine metabolism.cfa00500=Starch and sucrose metabolism.cfa00740=Riboflavin metabolism.cfa00760=Nicotinate and nicotinamide metabolism.cfa00770=Pantothenate and CoA biosynthesis.cfa01100=Metabolic pathways
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75 ENSCAFT00000000144 483960 N
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76 ENSCAFT00000000160 610160 N
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77 ENSCAFT00000000215 U N
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78 etc.
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79
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80 </help>
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81 </tool>